Rosetta 3.3
|
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/Pose.hh>
#include <basic/options/util.hh>
#include <protocols/init.hh>
#include <core/import_pose/import_pose.hh>
#include <numeric/xyzVector.hh>
#include <numeric/random/random.hh>
#include <utility/vector1.hh>
#include <utility/file/FileName.hh>
#include <basic/Tracer.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <cstdlib>
#include <fstream>
#include <iostream>
#include <string>
#include <sstream>
#include <cmath>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/ddg.OptionKeys.gen.hh>
#include <core/chemical/ResidueType.hh>
Typedefs | |
typedef std::vector< Real > | ddGs |
Functions | |
std::ostream & | writeYamlValue (std::ostream &S, std::string name, core::Real value) |
std::ostream & | writeYamlValue (std::ostream &S, std::string name, bool value) |
Real | sum (ddGs &scores_to_sum) |
Real | average (utility::vector1< Real > &scores_to_average) |
Size | store_energies (ObjexxFCL::FArray2D< Real > &two_d_e_arrays, scoring::ScoreFunction &s, pose::Pose &p, Size next_index, Size size_to_expect) |
Size | average_score_components (ObjexxFCL::FArray2D< Real > &scores_to_average, utility::vector1< Real > &averaged_scores) |
Real | correlation_coefficient (utility::vector1< Real > sim, utility::vector1< Real > exp) |
void | correlation (std::string ddg_out) |
int | main (int argc, char *argv[]) |
Variables | |
static numeric::random::RandomGenerator | RG (946571) |
static basic::Tracer | TR ("apps.pilot.yiliu.ddg") |
Real average | ( | utility::vector1< Real > & | scores_to_average | ) |
References color_pdb::i, and sum().
Referenced by main(), run_pep_prep(), and shift_angles().
Size average_score_components | ( | ObjexxFCL::FArray2D< Real > & | scores_to_average, |
utility::vector1< Real > & | averaged_scores | ||
) |
References color_pdb::i, ObjexxFCL::FArray2D< T >::l1(), ObjexxFCL::FArray2D< T >::l2(), ObjexxFCL::FArray2D< T >::u1(), and ObjexxFCL::FArray2D< T >::u2().
Referenced by main().
void correlation | ( | std::string | ddg_out | ) |
Real correlation_coefficient | ( | utility::vector1< Real > | sim, |
utility::vector1< Real > | exp | ||
) |
References utility::options::OptionKeys::options::exit, color_pdb::i, TR, and rosetta_py::utility::rankorder::x.
Referenced by correlation().
References average(), average_score_components(), begin, correlation(), utility::io::oc::cout, basic::options::OptionKeys::ddg::debug_output, basic::options::OptionKeys::ddg::dump_pdbs, utility::options::OptionKeys::options::exit, ObjexxFCL::fmt::F(), utility::filename(), color_pdb::i, basic::options::OptionKeys::in::in, src::init(), basic::options::OptionKeys::ddg::iterations, get_pdb::line, basic::options::OptionKeys::casp::num_iterations, basic::options::OptionKeys::out::file::o, option, options, basic::options::OptionKeys::canonical_sampling::out::out, basic::options::OptionKeys::loops::output_pdb, basic::options::OptionKeys::in::path::pdb, out::path::pdb(), PyMOL_demo::pose, NetLink::r, get_pdb::resnum, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), store_energies(), sum(), and basic::options::OptionKeys::casp::weight_file.
Size store_energies | ( | ObjexxFCL::FArray2D< Real > & | two_d_e_arrays, |
scoring::ScoreFunction & | s, | ||
pose::Pose & | p, | ||
Size | next_index, | ||
Size | size_to_expect | ||
) |
References begin, ObjexxFCL::FArray2D< T >::dimension(), end, color_pdb::i, and basic::options::OptionKeys::in::file::s.
Referenced by main().
Real sum | ( | ddGs & | scores_to_sum | ) |
std::ostream& writeYamlValue | ( | std::ostream & | S, |
std::string | name, | ||
core::Real | value | ||
) |
Referenced by correlation(), and statistics().
std::ostream& writeYamlValue | ( | std::ostream & | S, |
std::string | name, | ||
bool | value | ||
) |
numeric::random::RandomGenerator RG(946571) [static] |
Referenced by basic::setup_tag2string().
basic::Tracer TR("apps.pilot.yiliu.ddg") [static] |